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rsemeraro / XomeBlender

Generates synthetic cancer genomes with different contamination level and intra-tumor heterogeneity and devoid of any synthetic element
GNU General Public License v3.0
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InXalizer silent failure #4

Open genegolts opened 1 year ago

genegolts commented 1 year ago

Hello, I have install all of the dependencies and was able to kick off inxalizer with these parameters : -la clone -r $REF -scn 2 -vn 1000 -sa linear -t 8 -o $myOutput -vb 1

It runs for several hours, creates a clone.vcf file of ~2.6 million lines, but then dies. The stdout ends with the following:

InXalizer: error: [Errno 2] No such file or directory: '/rnd/users/ggoltsman/JIRA/PIP-4700.in-silico_NA1278_mutants/XomeBlender/Fatal'

It seems like some intermediate dependency fails to be generated here. Please advice.

p.s. my input bam file is sorted and indexed with samtools v1.15.1

rsemeraro commented 1 year ago

Hello, could you pass me the bam file or a subsampled version of the same, to make some tests? Thanks.